The story takes place in the ideal city "NO.6" in 2013. Shion was judged as having "highest-ranked intelligence" when he was two years old and was allowed to live in the luxurious area "Cronos".

On his twelfth birthday, he met a boy called "Nezumi," who had escaped from a reformatory. Shion protected him, but the Public Security Bureau deprived Shion of all his privileges and expelled him from Cronos to "Lost Town".

Four years after the banishment, a mysterious accident leads Shion to the secret of the city NO.6.